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kundajelab / chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline
BSD 3-Clause "New" or "Revised" License
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Installing Genomes: TwoBitToFa not found #13

Closed AHCChan closed 6 years ago

AHCChan commented 7 years ago

Hi!

I installed the pipeline then tried to install a genome but came across this

install_genome_data.sh: line 171: twoBitToFa: command not found

I tried to install twobittofa using conda but ran into some issues. Is there any workaround?

leepc12 commented 7 years ago

Hello,

Did you follow the installation instruction for dependencies ( https://github.com/kundajelab/chipseq_pipeline#dependencies)? twoBitToFa is included in that.

It is not recommended to manually install dependencies. It's very tricky. The pipeline needs two conda environments for each python version 2/3 and some required softwares are not available on official conda repos.

Please use the dependency installer in the repo.

Thanks,

Jin

On Thu, Apr 27, 2017 at 2:55 AM, AHCChan notifications@github.com wrote:

Hi!

I installed the pipeline then tried to install a genome but came across this

install_genome_data.sh: line 171: twoBitToFa: command not found

I tried to install twobittofa using conda but ran into some issues. Is there any workaround?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kundajelab/chipseq_pipeline/issues/13, or mute the thread https://github.com/notifications/unsubscribe-auth/AIOd_IMQw8yK5qQOxMdHEPeyoDrNJ96jks5r0GYmgaJpZM4NJ_pt .

AHCChan commented 7 years ago

Hello,

Yes, I followed the installation instructions and used the dependency installer (install_dependencies.sh). I received a message saying that the dependency installation was successful

Finished processing dependencies for idr==2.0.3 == Installing dependencies has been successfully done. ==

For good measure, I uninstalled the dependencies and ran the dependency installation script again. I still get the same error when trying to install a genome.

install_genome_data.sh: line 171: twoBitToFa: command not found

Many thanks,

Angelo

leepc12 commented 7 years ago

It's fixed. Please try with the latest code.

AHCChan commented 7 years ago

Hi, sorry to bother you again. I tried with the new code and received this message:

Extracting/processing data files... Building bwa index... [bwa_index] Pack FASTA... 47.76 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=5451530962, availableWord=395589816 [BWTIncConstructFromPacked] 10 iterations done. 99999986 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999986 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999986 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999986 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999986 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999986 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999986 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999986 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999986 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999986 characters processed. install_genome_data.sh: line 221: 20197 Killed bwa index ${REF_FA_PREFIX}

leepc12 commented 7 years ago

Did you run the installer script on a login node (if you are working on a cluster)? Does your computer have enough memory to run bwa index?